Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1038/s41598-019-54382-w http://hdl.handle.net/11449/197564 |
Resumo: | This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel. |
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Repositório Institucional da UNESP |
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spelling |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattleThis study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, Sao Paulo, SP, BrazilCtr Univ Adamantina, Sao Paulo, SP, BrazilInst Zootecnia, Sao Paulo, SP, BrazilUniv Fed Paraiba, Ctr Ciencias Agr, Areia, PB, BrazilEmbrapa Pecuaria Sudeste, Sao Paulo, SP, BrazilUniv Sao Paulo, Dept Zootecnia, Escola Super Agr Luiz de Queiroz, Sao Paulo, SP, BrazilMichigan State Univ, Dept Anim Sci, Coll Agr & Nat Resources, E Lansing, MI 48824 USAUniv Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, Sao Paulo, SP, BrazilFAPESP: 2015/25096-6FAPESP: 2016/22940-3FAPESP: 2013/20091-0FAPESP: 2013/19335-2FAPESP: 2012/23638-8Nature Publishing GroupUniversidade Estadual Paulista (Unesp)Ctr Univ AdamantinaInst ZootecniaUniv Fed ParaibaEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade de São Paulo (USP)Michigan State UnivBernardes, Priscila Arrigucci [UNESP]Nascimento, Guilherme Batista doSavegnago, Rodrigo PelicioniBuzanskas, Marcos EliWatanabe, Rafael Nakamura [UNESP]Almeida Regitano, Luciana Correia deCoutinho, Luiz LehmannGondro, CedricMunari, Danisio Prado [UNESP]2020-12-11T03:46:41Z2020-12-11T03:46:41Z2019-11-29info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article10http://dx.doi.org/10.1038/s41598-019-54382-wScientific Reports. London: Nature Publishing Group, v. 9, 10 p., 2019.2045-2322http://hdl.handle.net/11449/19756410.1038/s41598-019-54382-wWOS:000499892600001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScientific Reportsinfo:eu-repo/semantics/openAccess2024-06-06T13:42:21Zoai:repositorio.unesp.br:11449/197564Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:55:56.123867Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
title |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
spellingShingle |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle Bernardes, Priscila Arrigucci [UNESP] |
title_short |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
title_full |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
title_fullStr |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
title_full_unstemmed |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
title_sort |
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle |
author |
Bernardes, Priscila Arrigucci [UNESP] |
author_facet |
Bernardes, Priscila Arrigucci [UNESP] Nascimento, Guilherme Batista do Savegnago, Rodrigo Pelicioni Buzanskas, Marcos Eli Watanabe, Rafael Nakamura [UNESP] Almeida Regitano, Luciana Correia de Coutinho, Luiz Lehmann Gondro, Cedric Munari, Danisio Prado [UNESP] |
author_role |
author |
author2 |
Nascimento, Guilherme Batista do Savegnago, Rodrigo Pelicioni Buzanskas, Marcos Eli Watanabe, Rafael Nakamura [UNESP] Almeida Regitano, Luciana Correia de Coutinho, Luiz Lehmann Gondro, Cedric Munari, Danisio Prado [UNESP] |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Ctr Univ Adamantina Inst Zootecnia Univ Fed Paraiba Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Universidade de São Paulo (USP) Michigan State Univ |
dc.contributor.author.fl_str_mv |
Bernardes, Priscila Arrigucci [UNESP] Nascimento, Guilherme Batista do Savegnago, Rodrigo Pelicioni Buzanskas, Marcos Eli Watanabe, Rafael Nakamura [UNESP] Almeida Regitano, Luciana Correia de Coutinho, Luiz Lehmann Gondro, Cedric Munari, Danisio Prado [UNESP] |
description |
This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-11-29 2020-12-11T03:46:41Z 2020-12-11T03:46:41Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1038/s41598-019-54382-w Scientific Reports. London: Nature Publishing Group, v. 9, 10 p., 2019. 2045-2322 http://hdl.handle.net/11449/197564 10.1038/s41598-019-54382-w WOS:000499892600001 |
url |
http://dx.doi.org/10.1038/s41598-019-54382-w http://hdl.handle.net/11449/197564 |
identifier_str_mv |
Scientific Reports. London: Nature Publishing Group, v. 9, 10 p., 2019. 2045-2322 10.1038/s41598-019-54382-w WOS:000499892600001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Scientific Reports |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
10 |
dc.publisher.none.fl_str_mv |
Nature Publishing Group |
publisher.none.fl_str_mv |
Nature Publishing Group |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128437189083136 |